Gov. Andrew M. Cuomo declared a state of emergency at the New York City Housing Authority on Monday and ordered an independent monitor be appointed to oversee and expedite repairs to the agency’s deteriorating buildings, where 400,000 New Yorkers live.

The executive order was the latest salvo in an escalating conflict between the governor and Mayor Bill de Blasio’s administration over the management of the beleaguered housing authority, the largest in the country.

For years the authority has been struggling with budgetary troubles and has neglected repairs. Those maintenance failures came to a head this winter when thousands of residents were left without heat and water.

The governor first drew attention to the agency’s shortcomings last month, when he visited a housing complex in the Bronx and hinted he might declare a state of emergency to address the unhealthy conditions he found.

The mayor suggested Mr. Cuomo was trying “to score political points” and challenged him to come up with a constructive plan.

Mr. de Blasio was conspicuously absent Monday as Mr. Cuomo signed the order on a crowded indoor basketball court in the Johnson Houses in East Harlem, flanked by other city officials who have criticized the mayor’s management of Nycha.

“Delivering money to Nycha is like throwing it out the window,” Mr. Cuomo told reporters after the signing. “I’m not going to hand over money to an entity that can’t spend the money — that was the entire point.”

The declaration appoints an independent monitor that will oversee how Nycha spends the $250 million the state appropriated to the agency in the budget signed this weekend. The monitor will also oversee $350 million the state has pledged in previous years but has not released to the agency, as well as any unspent money appropriated by the city.

“It is very important that that money not get caught up in any bureaucracy,” Mr. Cuomo said.

Mayor de Blasio, during his weekly interview on NY1 Monday evening, said he feared the order would create “a whole lot of bureaucracy.” Now, he added, the governor is responsible for giving Nycha half a billion dollars.

The independent monitor would have broad powers over Nycha and could make changes to its management, a state official said. But the monitor’s primary task would be to expedite repairs to problems like broken boilers, mold and lead paint, which pose a threat to public health.

According to the order, the independent monitor must be appointed within the next 60 days and will be chosen by the mayor, the City Council speaker and the president of the Citywide Council of Presidents, a group of tenant leaders chosen by Nycha residents, which sued the agency in February.

The monitor would then have 30 days to select a private contractor for repairs, and certain procurement rules would be waived to speed along projects. Nycha would have no say in the selection of contractors.

Mr. Cuomo’s order was unsparing in its critique, asserting “the conditions of habitability at Nycha-managed residential properties constitute a public nuisance affecting the security of life and health in the City of New York” and that a “disaster is imminent for which the affected local government is unable to respond adequately.”

The governor’s visit to the Johnson Houses was his fourth visit to a public housing complex since March 12. He made the announcement on the same spot where, three years ago, Mr. de Blasio and Shola Olatoye, the agency’s embattled chairwoman, unveiled NextGen Nycha, the administration’s ambitious plan to reverse the agency’s shortfalls.

Several city officials who have been reliable antagonists of the mayor joined Mr. Cuomo and praised his decision, including Scott M. Stringer, the city comptroller, and Councilman Ritchie Torres, as well as those seeking to assert independence from him, like Corey Johnson, the council speaker, and Letitia James, the public advocate.

After the governor’s announcement, the mayor and the governor spoke, by phone, for the first time in more than two weeks, according to City Hall. City Hall was not given a copy of the emergency order before the governor signed it.

City officials had told the state Nycha intended to use the $250 million in new aid to replace “63 poorly rated boilers” in 14 housing developments, but it was unclear if the monitor would take those priorities into consideration.

Mr. Cuomo’s announcement comes roughly two weeks after the federal Department of Housing and Urban Development told the city’s housing authority that it would no longer be able to draw federal funds without approval, placing the authority on a so-called “zero threshold.”

That development came after months of back-and-forth between agencies, stemming from the revelation that Nycha had been filing false paperwork to the federal government related to lead-paint inspections. The failures were part of what the housing department called a “fraud investigation” into Nycha by the United States attorney for the Southern District of New York.

Those allegations led to a public outcry and calls for Ms. Olatoye’s resignation, but Mr. de Blasio has stood by the chairwoman’s side.

The city has been negotiating with federal prosecutors for months but has yet to reach a settlement. Mayor de Blasio has said the negotiations could result in a federal monitor for the Housing Authority. Last year, the federal housing department warned of penalties if Nycha did not reach a settlement with the United States attorney, or come up with a health and safety plan to address concerns over lead paint and other issues with the physical state its apartments and buildings. Those deadlines passed last month.

“As a consequence of its failure to produce this corrective plan, H.U.D. will now review and approve all expenditures from Nycha’s Capital Fund,” the department said in a statement.